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S13-like H2TH domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   S13-like H2TH domain [ 81297]
Superfamily:   S13-like H2TH domain [ 46946] (3)
Families:   Ribosomal protein S13 [ 46947]
  Middle domain of MutM-like DNA repair proteins [ 81626] (3)
  Topoisomerase VI-B subunit middle domain [ 81705]


Superfamily statistics
Genomes (3,252) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 7,775 57,043 25
Proteins 7,770 56,997 25


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Isomerases1Least InformativeInherited
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases0InformativeDirect
Enzyme Commission (EC)Sole sub-subclass for isomerases that do not belon1InformativeInherited
Enzyme Commission (EC)DNA-formamidopyrimidine glycosylase0Highly InformativeDirect
Enzyme Commission (EC)DNA-(apurinic or apyrimidinic site) lyase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect
Yeast Phenotype (YP)morphology0Moderately InformativeDirect
Yeast Phenotype (YP)nutrient utilization0Moderately InformativeDirect
Yeast Phenotype (YP)vegetative growth0InformativeDirect
Yeast Phenotype (YP)heat sensitivity0InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Glycosylases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0InformativeDirect
Enzyme Commission (EC)DNA-(apurinic or apyrimidinic site) lyase0Highly InformativeDirect
Enzyme Commission (EC)DNA topoisomerase (ATP-hydrolyzing)0.00000000000004292Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR010979 SSF46946 Protein matches
Abstract

Ribosomal protein S13 is one of the proteins from the small ribosomal subunit [PubMed12464183]. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. S13 contains thee helices and a beta-hairpin in the core of the protein, which form a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension.

This H2TH motif can be found in other proteins as well. In the DNA repair protein, MutM (formamidopyrimidine DNA glycosylase; Fpg), the middle domain contains the H2TH motif. MutM is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidatively damaged bases (N-glycosylase activity) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity) [PubMed10921868]. Other repair enzymes, such as Escherichia coli Endonuclease VIII that excises oxidized pyrimidines from DNA, also contain a DNA-binding H2TH motif within the middle domain. The H2TH domains of these repair proteins are only peripherally involved in binding DNA; their primary function may be simply to position the N-terminal lobe and C-terminal zinc finger domain of the glycosylases for interactions with DNA.

The middle domain of topoisomerase IV-B subunit contains a H2TH motif that is structurally related to the DNA repair proteins. Although the H2TH domain appears to be retained in all archaeal and plant typeż IIB topoisomerases identified to date, it has no known function and has not been observed in other topoisomerase families [PubMed12505993].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 9 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a S13-like H2TH domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 9 hidden Markov models representing the S13-like H2TH domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]